Use this URL to cite or link to this record in EThOS: http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.693954
Title: Topological investigation of bacterial site-specific recombination and genome differentiation in ciliates
Author: Valencia Gomez, Karin Andrea
Awarding Body: Imperial College London
Current Institution: Imperial College London
Date of Award: 2013
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Abstract:
Since the double helical structure of DNA was discovered in 1953, significant progress has been made towards the understanding of the science of the molecule of life. It is now clear that topology can strongly in infuence, or even drive its functionality [47]. The underlying motivation of this thesis is to investigate the topology of DNA during: (i) bacterial site-specific recombination; and (ii) developmental genome rearrangements in ciliates. (i) A model of site-specific recombination, that predicts and characterises the exact topology of products from non-distributive reactions on DNA twist knot substrates is developed. This is a generalisation of work by Buck and Flapan in [19] where the same question was considered for topologically simpler substrates. It is shown that such products fall within a well understood family of knots and links called Montesinos knots and links. In the common case where products have minimal crossing number one more than the substrate it is proved that the product topology is more tightly prescribed. It is further shown that the number of possible product knots and links decreases exponentially as a function of the topological complexity of the product, which can greatly aid their experimental identification. (ii) Massive genome-wide rearrangements in some binucleate ciliates are modelled by rigid- vertex graphs, first proposed in [4]. This work builds on that of Jonoska and collaborators, who have investigated graph-theoretic complexities of these model, by now considering their topology. The genus range of a family of rigid vertex graph that may represent naturally occurring patterns of some gene rearrangements that have multiple repetitions (as many as to over 20 recombination sites) is characterised. The genus ranges of other families of rigid vertex graph are discussed.
Supervisor: Not available Sponsor: Not available
Qualification Name: Thesis (Ph.D.) Qualification Level: Doctoral
EThOS ID: uk.bl.ethos.693954  DOI: Not available
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